William H. Fink

Frozen fragment reduced variational space analysis of hydrogen bonding interactions. Application to the water dimer

Abstract A reduced variational space method is presented for analyzing hydrogen bonding interactions in terms of Coulomb and exchange, polarizability, and charge-transfer components. The method relies on the use of SCF optimized monomer orbitais in dimer calculations in which the wavefunction of one monomer is held frozen while the other is optimized with a basis set including selected subsets of the unoccupied monomer orbitals. Freezing the monomer wavefunctions allows the polarizability and charge-transfer interactions to be ascribed to specific monomers. Applications are presented for the interaction energy and dipole moment of the water dimer.

Stable, Monomeric Imides of Aluminum and Gallium: Synthesis and Characterization of [{HC(MeCDippN)2}MN‐2,6‐Trip2C6H3] (M=Al or Ga; Dipp=2,6‐iPr2C6H3; Trip=2,4,6‐iPr3C6H2)

A short Ga-N bond with double-bond character is displayed by the first monomeric imide of gallium, which was obtained by the reaction of [{HC(MeCDippN)2 }M:] (Dipp=2,6-iPr2 C6 H3 , M=Ga; see picture) with N3 -2,6-Trip2 C6 H3 (Trip=2,4,6-iPr3 C6 H2 ). The analogous aluminum (M=Al) compound is also readily available.

Dynamics of Antifreeze Glycoproteins in the Presence of Ice

Antifreeze glycoproteins from the Greenland cod Boreogadus saida were dimethylated at the N-terminus (m*AFGP) and their dynamics and conformational properties were studied in the presence of ice using (13)C-NMR and FTIR spectroscopy. (13)C-NMR experiments of m*AFGP in D(2)O, in H(2)O, and of freeze-dried m*AFGP were performed as a function of temperature. Dynamic parameters ((1)H T(1 rho) and T(CH)) obtained by varying the contact time revealed notable differences in the motional properties of AFGP between the different states. AFGP/ice dynamics was dominated by fast-scale motions (nanosecond to picosecond time scale), suggesting that the relaxation is markedly affected by the protein hydration. The data suggest that AFGP adopts a similar type of three-dimensional fold both in the presence of ice and in the freeze-dried state. FTIR studies of the amide I band did not show a single prevailing secondary structure in the frozen state. The high number of conformers suggests a high flexibility, and possibly reflects the necessity to expose more ice-binding groups. The data suggest that the effect of hydration on the local mobility of AFGP and the lack of significant change in the backbone conformation in the frozen state may play a role in inhibiting the ice crystal growth.

The Dynamics, Structure, and Conformational Free Energy of Proline-Containing Antifreeze Glycoprotein

Recent NMR studies of the solution structure of the 14-amino acid antifreeze glycoprotein AFGP-8 have concluded that the molecule lacks long-range order. The implication that an apparently unstructured molecule can still have a very precise function as a freezing inhibitor seems startling at first consideration. To gain insight into the nature of conformations and motions in AFGP-8, we have undertaken molecular dynamics simulations augmented with free energy calculations using a continuum solvation model. Starting from 10 different NMR structures, 20 ns of dynamics of AFGP were explored. The dynamics show that AFGP structure is composed of four segments, joined by very flexible pivots positioned at alanine 5, 8, and 11. The dynamics also show that the presence of prolines in this small AFGP structure facilitates the adoption of the poly-proline II structure as its overall conformation, although AFGP does adopt other conformations during the course of dynamics as well. The free energies calculated using a continuum solvation model show that the lowest free energy conformations, while being energetically equal, are drastically different in conformations. In other words, this AFGP molecule has many structurally distinct and energetically equal minima in its energy landscape. In addition, conformational, energetic, and hydrogen bond analyses suggest that the intramolecular hydrogen bonds between the N-acetyl group and the protein backbone are an important integral part of the overall stability of the AFGP molecule. The relevance of these findings to the mechanism of freezing inhibition is discussed.

Theoretical Predictions on the Structures of Diimide

The LCAO MO SCF wavefunctions have been determined for the ground states of the isomeric forms of diimide. Molecular geometries for trans(1Ag)‐, cis(1A1)‐diimide, and 1, 1‐dihydrodiazine were deduced through the most detailed systematic geometry search to date on the diimide molecule. Contrary to the results from semiempirical calculations where cis‐diimide has been predicted to be 4.5–8.5 kcal/mole more stable than the trans form, this calculation shows that the trans form is more stable. Furthermore, contrary to the common assumptions, the bond distances and bond angles are found to be different for different isomeric forms, due to the difference in electronic and nuclear repulsive forces. A discussion is made on the ultraviolet and infrared experimental results and comparison is made between the trans‐N2H2 closed‐shell 1Ag state and the open‐shell 3Bg state at the theoretically calculated and the experimentally obtained configurations. The calculated force constants and dipole moment of cis‐N2H2 are re...

Approach to Partially Predetermining Molecular Electronic Structure. The Li He Interaction Potential

The utility of the simplest possible formulation of the group function method of McWeeney for electronic structure calculations of systems involving identifiable molecular subunits is discussed. The method is applied to the calculation of the Li He interaction potential in order to provide a means of identifying the interaction energy as an electrostatic interaction, a backbonding interaction and a full molecular orbital SCF interaction. Some interesting results for methods of integrated charge analysis are also discussed.

Brownian dynamics simulations of sequence-dependent duplex denaturation in dynamically superhelical DNA.

The topological state of DNA in vivo is dynamically regulated by a number of processes that involve interactions with bound proteins. In one such process, the tracking of RNA polymerase along the double helix during transcription, restriction of rotational motion of the polymerase and associated structures, generates waves of overtwist downstream and undertwist upstream from the site of transcription. The resulting superhelical stress is often sufficient to drive double-stranded DNA into a denatured state at locations such as promoters and origins of replication, where sequence-specific duplex opening is a prerequisite for biological function. In this way, transcription and other events that actively supercoil the DNA provide a mechanism for dynamically coupling genetic activity with regulatory and other cellular processes. Although computer modeling has provided insight into the equilibrium dynamics of DNA supercoiling, to date no model has appeared for simulating sequence-dependent DNA strand separation under the nonequilibrium conditions imposed by the dynamic introduction of torsional stress. Here, we introduce such a model and present results from an initial set of computer simulations in which the sequences of dynamically superhelical, 147 base pair DNA circles were systematically altered in order to probe the accuracy with which the model can predict location, extent, and time of stress-induced duplex denaturation. The results agree both with well-tested statistical mechanical calculations and with available experimental information. Additionally, we find that sites susceptible to denaturation show a propensity for localizing to supercoil apices, suggesting that base sequence determines locations of strand separation not only through the energetics of interstrand interactions, but also by influencing the geometry of supercoiling.

Photodissociation of the dibromomethane cation at 355 nm by means of ion velocity imaging

The photodissociation dynamics of the dibromomethane cation, CH2Br2+, have been studied by means of ion velocity imaging and time-of-flight mass spectroscopy methods at 355 nm. The dibromomethane cation is produced through the direct ionization of the neutral molecule with a pulsed 118 nm laser. The translational energy distribution shows that the CH2Br+ fragment is formed in highly vibrationally excited states with two distinguished dissociation channels following a parallel excitation from 2b2 to 3b2 of the parent ion. The broad fast speed distribution is fit with two Gaussian functions, from which a branching ratio of Br*(2P1/2) to Br(2P3/2) is determined as 2.2:1. The sharp peak with very slow speed was modeled with a Boltzmann distribution with a temperature of 300 K. This channel contributes ∼4.5% to the reaction and is proposed to proceed on the ground state surface following internal conversion. Ab initio calculations for both the parent and the fragment ions have been performed that strongly supp...

Calculations of the Ground and Excited State Energies of NO2

Calculations of fifteen different states of nitrogen dioxide in the ground state equilibrium geometry are reported. Nine of these are SCF calculations; the remainder are roots of a configuration interaction calculation performed using the SCF orbitals calculated for the ground state as an expansion set. The configuration interaction was performed within the A1 irreducible representation in order specifically to locate the first excited state of the same symmetry species as the ground state. A 3s‐like atomic orbital was included in the basis set in order to more adequately represent molecular orbitals tending toward Rydberg levels. The SCF energy for the ground state was calculated to be − 203.907 a.u. The configuration interaction calculated yielded an energy of − 203.949 a.u. for the ground state. Probable assignments of the electronic transitions involved in the spectrum of nitrogen dioxide are discussed.

A thorough analysis and exposition of the four-index transformation

Abstract The nature of two-electron integral transformations as a major stumbling block to configuration interaction calculations is discussed. An N5 general procedure utilizing positional algorithms for all members of specially ordered lists of partial summations is presented. Theoretical analysis detailing sequencing and calculational algorithms is included, augmented by results of FORTRAN programmed versions of the method. Two program versions differing in the manner of dividing the partially summed integrals into blocks give practical orders N 5 .5±0.2 and N 6.23±0.05 , the former approaching theoretical order.